Smeargle was from Generation II, not III. The rest of the Pokemon on that top five list are generationally correct, but if you want to pick a #1 favorite from GenIII, take Smeargle off of that list and bump Flygon up a notch.

Smeargle appeared in Emerald specifically due to public outcry against GenIII's incompatibility with the previous two generations, making many player's life works moot point. He was one of the few things not remedied by FRLG.

Anyway, to stay on topic, I'd say Mudkip, Gardevoir and Blaziken are my favorites, but in no particular order.

I really like Blaziken and Kyogre. I had no idea how reliable they would be when I started Sapphire version, but they helped me out of several tight spots. I always used them to challenge the Elite Four because it was almost guaranteed that I would defeat them in under 10 minutes. They're just great Pokemon.